GeoChip 4.2 hybridization
Fungal functional genes were
accessed by GeoChip 4.2 (Roche NimbleGen Inc., Madison, WI, USA), which
is a functional microarray containing more than 107,950 oligonucleotide
probes of 792 bacterial, archaeal and fungal genes associated with C,
nitrogen (N), phosphorus (P) and sulfur (S) cycling, stress, virulence,
energy process, to name a few. These oligonucleotide probes are
designed from functional gene sequences of microbial organisms with
known taxonomy in the NCBI database (He et al., 2007). Before
hybridization, 1 μg of purified DNA was labeled with the fluorescent dye
Cy3. After overnight hybridization, unbound DNA was removed. Then
GeoChip was scanned by a NimbleGen MS 200 Microarray Scanner (Roche,
Basel, Switzerland) at 532 nm and 635 nm. Probes with signal-to-noise
ratio lower than 2 were considered to be unreliable and hence removed.
The normalized signal intensity of each detected probe was calculated by
dividing total signal intensity by each detected probe and
log-transformed.